Version Information
Current Version: | 1.8.2beta |
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Release Date: | May 2025 |
License: | Mozilla 2 Open-Source License |
Download
Description | i2b2 Release Version | Minimum Version Required | Download Link |
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Files to install the i2b2 server to 1.8.2beta | 1.8.2beta | 1.7.09c | |
Files to install the i2b2 db instance to 1.8.2beta | 1.8.2beta | 1.7.09c | i2b2 1.8.2beta data install Source code |
Files to install the webclient | 1.8.2beta | i2b2 1.8.2beta Webclient install Source code |
Notes
If you are running your application on JBoss, please upgrade Wildfly to 34 and java to 17 versions before proceeding with the upgrade
Install/Upgrade Instructions
Below are Step-by-Step Instructions after you have upgraded to Wildfly.
Initial Steps:
- Download the binary install distribution from i2b2 1.8.2 Core Server install Source code
- Extract the download file to a folder outside of your existing i2b2 installation folder
Then, follow the steps below to install i2b2 server, database instance and the webclient.
Steps to Install i2b2 Server
In the following instructions the variable {version } refers to your version of Wildfly installed. We now support Wildfly 34 version.
Stop WildFly
Backup existing deployment directory containing i2b2.war file
Install Core i2b2 Server
- Install Java 17
- Copy the entire wildfly-34.0.1.Final folder to your /opt folder.
Linux: cp –r wildfly-34.0.1.Final /opt
Windows: xcopy /E wildfly-34.0.1.Final C:\opt
Update datasource (*-ds.xml) files
In your deployment directory, opt/wildfly-34.0.#.Final/standalone/deployments:
Edit the following files crc-ds.xml, ont-ds.xml, pm-ds.xml, work-ds.xml with your database info
Oracle | SQL Server | PostgreSQL |
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<driver>ojdbc8.jar</driver> | <driver>mssql-jdbc-12.4.2jre8.jar</driver> | <driver>postgresql42.7.1jar</driver> |
Migrate cell properties to 1.8.2 if needed. In 1.7.12, cell properties have been moved to the database, in a table called hive_cell_params. If any cell properties were previously changed, they will need to be manually updated in the database. After this, the properties files can be deleted to prevent confusion.
More documentation on setting cell properties is available at this page. Most commonly, the AGG_SERVICE_ACCOUNT password will need to be updated. Generally, the cell URLs do not need to be configured anymore, as the hostname and port is now auto-detected.
Properties files are stored at /opt/wildfly-{version}.Final/standalone/configuration/ on Linux and c:\opt\wildfly-{version}.Final\standalone\configuration\ on Windows. The table can be edited with a SQL editor in hive_cell_params.
Steps to Setup/Upgrade i2b2 database
Steps to perform db upgrade if your
- Backup your existing data folder
- Copy all the folders created by extracting the latest version into your existing data Upgrade folder. This will replace existing Crcdata, Hivedata, Metadata, PMdata folders. Example: Downloads\i2b2core-upgrade-182beta\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-8\Upgrade\.
- Copy the db.properties files from your back up into the respective locations (namely Crcdata, Hivedata, Metadata, PMdata )
- Open the command prompt and navigate to each cell folder and run the following upgrade ant commands on your i2b2 database instance, where {db} can be Oracle, sqlserver or postgresql.
Alternative to above Step, you can run individual SQL scripts on your db instance in place of ant commands. - In datafolder\Release_1-8\Upgrade\ run the ant commands under each individual cell folder as below
Upgrade db From Build | Upgrade db to Latest build |
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1.7.09c | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-09c upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-12a In the Pmdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-09c |
1.7.10 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-12a |
1.7.11 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_table_release_1-7-12a In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a |
1.7.12a | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a |
1.7.13 | For Oracle and Postgres, no database upgrade is required. If using SQL Server, reload the following stored procedures: In the Metadata folder run the following ant command: ant -f data_build.xml rebuild_procedures |
1.8.0 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-8-0 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-8-0 In the Metadata folder run the following ant command: ant -f data_build.xml rebuild_procedures |
1.8.1 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-8-1 In the Metadata folder run the following ant command: ant -f data_build.xml rebuild_procedures |
HIVE_CELL_PARAMS configuration
Check HIVE_CELL_PARAMS table is updated with cell properties parameters as detailed here
Steps to Upgrade i2b2 Webclient
Backup existing webclient folder to a different location outside of your current webclient installation folder
Install new webclient
- Extract the i2b2 1.8.2beta Webclient upgrade Source code
- Replace your existing webclient folder on your web server with the extracted new webclient folder
i2b2_config_data.js has been renamed to i2b2_config_domain.json. Edit the i2b2_config_domain.json using your existing i2b2_config_data.js from your backed up web directory. Details are provided here
Backup your entire webclient folder before proceeding with webclient upgrade
Start WildFly
You can either run WildFly standalone or as a service.
Verify Your Upgrade
Test Webclient
Navigate to your local i2b2 Web Client in your preferred browser and verify you are able to log on and perform standard i2b2 functions. (e.g. Run queries, retrieve previous queries, view breakdowns, etc.)